Hull will not be expelled from this year's Challenge Cup but could face a heavy fine for fielding an ineligible player in the last two rounds.
Prop Jamie Thackray rejoined Hull from Leeds on 27 March, more than three weeks after the deadline to register players for the competition.
Thackray played against Rochdale and Widnes in the fourth and fifth rounds.
But the RFL admitted that there were no specific penalty for playing an ineligible player.
The RFL said the breach was a "very serious matter" and suggested that the competition's rules would be tightened up to prevent a reoccurrence.
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Hull FC will now face Bradford Bulls in the quarter-final as planned.
A RFL statement read: "In view of the absence of a mandatory provision, the RFL board determined that the results of the Carnegie Challenge Cup fourth and fifth-round matches involving Hull FC will stand and the club will continue in the competition.
"It is, however, clear that playing an ineligible player is a serious breach of the operational rules and the board has referred the matter to the RFL compliance manager to deal with under the misconduct rules.
"The RFL board intends to review the operational rules relating to competitions and will consider whether the rules should be amended so that offences of this nature will lead to mandatory expulsion from the cup in future seasons."
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